{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3075NNHV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3075NNHV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7299CMAO](/in-vitro-systems/IGVFSM7299CMAO/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM7299CMAO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7299CMAO](/in-vitro-systems/IGVFSM7299CMAO/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM7299CMAO/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3075NNHV](/auxiliary-sets/IGVFDS3075NNHV/) has sequence file(s) [IGVFFI2105TWRS](/sequence-files/IGVFFI2105TWRS/), [IGVFFI1963MCVJ](/sequence-files/IGVFFI1963MCVJ/), [IGVFFI0782BNFN](/sequence-files/IGVFFI0782BNFN/), [IGVFFI4660XHJF](/sequence-files/IGVFFI4660XHJF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3075NNHV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3075NNHV](/auxiliary-sets/IGVFDS3075NNHV/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS3075NNHV/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-16T17:59:36.682525+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2105TWRS/",
"accession": "IGVFFI2105TWRS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:32.120700+00:00",
"file_format": "fastq",
"file_size": 8010614,
"href": "/sequence-files/IGVFFI2105TWRS/@@download/IGVFFI2105TWRS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/597d22f0-67b3-4015-9b83-83b8403b9975/IGVFFI2105TWRS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinC-PCR1_S63_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4716JRCO/",
"accession": "IGVFFI4716JRCO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:23.393885+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4716JRCO/@@download/IGVFFI4716JRCO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/674651de-d530-4fa3-a5e3-64f2482c849f/IGVFFI4716JRCO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinC-PCR1_S63.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0755GMWU/",
"accession": "IGVFFI0755GMWU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:53.072175+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0755GMWU/@@download/IGVFFI0755GMWU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/13d2b372-a5c1-42c2-8042-d9c2177c2be4/IGVFFI0755GMWU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinC-PCR3_S159.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1963MCVJ/",
"accession": "IGVFFI1963MCVJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:48.603062+00:00",
"file_format": "fastq",
"file_size": 12442357,
"href": "/sequence-files/IGVFFI1963MCVJ/@@download/IGVFFI1963MCVJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/058faf06-714d-446b-a458-f11d3c6a8d7d/IGVFFI1963MCVJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinC-PCR2_S69_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0782BNFN/",
"accession": "IGVFFI0782BNFN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:12.292191+00:00",
"file_format": "fastq",
"file_size": 20259442,
"href": "/sequence-files/IGVFFI0782BNFN/@@download/IGVFFI0782BNFN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/0cf9c4f8-c82f-4ab3-b2c1-a09bd76828ba/IGVFFI0782BNFN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinC-PCR3_S159_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4660XHJF/",
"accession": "IGVFFI4660XHJF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:33.197425+00:00",
"file_format": "fastq",
"file_size": 22190543,
"href": "/sequence-files/IGVFFI4660XHJF/@@download/IGVFFI4660XHJF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/da04dda6-4bf0-4c79-85fe-b21ffb436eab/IGVFFI4660XHJF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinC-PCR4_S165_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5109OXAG/",
"accession": "IGVFFI5109OXAG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:38.168428+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI5109OXAG/@@download/IGVFFI5109OXAG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3b347ec4-e48d-4207-b46c-b9d2238c7159/IGVFFI5109OXAG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinC-PCR2_S69.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2830IKNI/",
"accession": "IGVFFI2830IKNI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:09.800136+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI2830IKNI/@@download/IGVFFI2830IKNI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7854d2ba-ea21-4ea3-b47a-c4863c7bb852/IGVFFI2830IKNI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinC-PCR4_S165.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8710ZSOZ/",
"accession": "IGVFDS8710ZSOZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:18.868768+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7299CMAO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7299CMAO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin C for 35-45% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:22:32.120700+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ba09c2df-253e-4c36-9c6f-10ec9a895b13"
}